Looking at molecular models in order to explore and understand them. Does not necessarily involve molecular modeling (changing the existing model). Macromolecules – Protein, DNA, RNA, or their complexes. 3-D view of different molecules on the computer.

1. MOLECULAR
VISUALIZATION
ALEN SHAJI
P1914015

2. INTRODUCTION
 Looking at molecular models in order to explore and understand them.
 Does not necessarily involve molecular modeling (changing the existing
model).
 Macromolecules – Protein, DNA, RNA, or their complexes.
 3-D view of different molecules on the computer.

3. REPRESENTATIONS OF MOLECULAR MODELS
ATOMIC REPRESENTATION
 It includes ball and stick, stick (wireframe), and spacefilling.
 These representations show positions of atoms and covalent bonds.

4. SLABBING
 A usefull way to see atomic details of a small part of a large macromolecular
model is to centre the moiety of interest, and then cut away front and back
portions of the molecules.
 It is usefull to see buried structures and their environments, such as the
hydrophobic core of a protein domain.
 It can be done using FirstGlance in Jmol.

5. SIMPLIFIED SCHEMATIC REPRESENTATIONS
BACKBONES
 Simplified representations of the polypeptide backbone or main chain, are
very helpful in understanding structure when it comes to large molecules such
as Proteins, DNA, RNA, and their complexes.
 Using FirstGlance in Jmol.

6. DISULFIDE BONDS
 FirstGlance in Jmol highlights disulfide bonds in one click, and has several
options for rendinering and coloring them.

7. COLOUR SCHEMES FOR MACROMOLECULES
 A set of standard color schemes for macromolecules, called DRuMS, was
released in 2000.
 Colors for chemical elements.

8. STRUCTURAL ANALYSIS
 Molecular function.
 Prediction of function.
 Experimental design to test predictions.

9. TYPES OF MOLECULAR VISUALIZATION
 WIRE FRAME MODEL.
 BALL AND STICK MODEL.
 RIBBON SHAPED MODEL.
 SPACE FILLING.
 SIMPLE HARMONIC MODEL.
 BACKBONE.
 SURFACE.

10. WIRE FRAME MODEL
 Skeletal form of molecules – represent as wires.
 Network of wire.
 Line represents the bonds.
 Shows individual bonds and corresponding angles.

11. RIBBON SHAPED MODEL
 Spherical or cylindrical ribbons.
 Display the folding and structure of proteins.

12. BALL AND STICK MODEL
 Ball represents the atoms.
 Stick represents the bonds.
 Shows atomic positions and bonds and volume.

13. SIMPLE HARMONIC MODEL
 Only represents grooves and projections in the molecules.

14. SPACE FILLING
 Spheres represents the electro cloud around nuclei of atoms.
 Relative size of atoms and groups show up clearly.
 Merged spheres represents the sharing of electrons.

15. RasMol
 Most frequently available tool.
 Derived from Raster and molecules.
 Molecular graphics programe.
 For visualizing proteins, nucleic acid and small molecules for which 3-D
structures is available.
 In order to display molecules, RasMol requires atomic coordinate file that
specifies the position of every atom in the molecule through its 3-D Cartesian
coordinates.
 RasMol accept this coordinate file variety of formats including Protein Data
Bank format.

16.  It provides user a choice of colour schemes and molecular representation.
 Additional features including test labelling for slected atoms, different colour
schemes of different parts of the molecule, zoom, rotation etc.

17. REFERENCE
 Jin Xiong (2007) Essential Bioinformatics, Cambridge University, PressIndia,
Pvt LTD.
 Wikipedia - Molecular Visualization, Bioinformatics.

18. THANK YOU